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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('InTAD_1.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing InTAD ────────────────────────────────────────────────────────────
✔ Package installed successfully
── InTAD session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpL5u0yM/filec3908481c5ac/InTAD
→ BiocVersion: 3.24
→ Package: InTAD
→ PackageVersion: 1.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/InTAD.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpL5u0yM/filec3908481c5ac/InTAD
→ installDir: /tmp/RtmpL5u0yM/filec39085e337053
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on InTAD ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: ChipOnChip,
Coverage
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (53%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of InTAD...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/combineSignalsInTAD.R (line 149, column 35)
    • ...
    • R/findCorrelation.R (line 71, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • combineSignalsInTAD.R (line 32, column 18)
    • ...
    • plotCorrelation.R (line 159, column 31)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/combineSignalsWithLoops.R (line 127, column 10)
    • ...
    • R/plotCorrelation.R (line 197, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/combineSignalsInTAD.R (line 150, column 13)
    • ...
    • R/plotCorrelation.R (line 36, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/combineSignalsWithLoops.R (line 94, column 46)
    • ...
    • F in R/combineSignalsWithLoops.R (line 108, column 48)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/combineSignalsWithLoops.R (line 128, column 11)
  • suppressWarnings() in R/findCorrelation.R (line 20, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
  The longest 5 functions are:
    • plotCorAcrossRef() (R/plotCorrelation.R): 114 lines
    • ...
    • newSigInTAD() (R/InTADSig-methods.R): 70 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • combineWithLoops.Rd
  • findCorFromLoops.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 28 lines (2%) are > 80 characters long.
  First few lines:
    • R/combineSignalsWithLoops.R#L9 #' @param fragmentLength In case the inp
    ...
    • ...
    • vignettes/InTAD.Rmd#L306 and Romano-Palumbo, L., 2015. Population ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 87 lines (5%) are not.
  First few lines:
    • R/combineSignalsInTAD.R#L113 stop("No overlaps found between si ...
    • ...
    • vignettes/InTAD.Rmd#L271 showCorVals = TRUE, sym ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | ℹ 15 NOTES
ℹ See the InTAD.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.